Sequence
atgc intronic sequence ATGC exonic sequencegtatgattacattttaccatacccttttgaaattattatgttttctgtgttttatttttgtaataatgcattagcgaattgatcattgatgatctggggtcttatttaagcgagtgttcatgtgaatttgcagCTGAGTAGTTGCTTCCTTGTGTGTATGAAAGATGATAGTATAGAGGGGATATACGAAACTTTGAAGGAGTGTGCTATCATCAGCAAATCAGCTGGAGGAA
Basic information
species | Glycine max |
transcript | GLYMA04G39500.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G39500.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 4
gtatgattacattttaccatacccttttgaaattattatgttttctgtgttttatttttgtaataatgcattagcgaattgatcattgatgatctggggtcttatttaagcgagtgttcatgtgaatttgcagCTGAGTAGTTGCTTCCTTGTGTGTATGAAAGATGATAGTATAGAGGGGATATACGAAACTTTGAAGGAGTGTGCTATCATCAGCAAATCAGCTGGAGGAA
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----------------------------------------------gtactgcacatttgaccagaaaaatcctagtcttggactctga--aattg----cttgcttactcttttattctctgcaat--gcagTTAAGCAGCTGTTTCCTTATCTGCATGAAAGATGACAGCATTGAGGGAATCTATGATACTTTGAAGGAATGTGCTGTCATAAGCAAATCTGCTGGAGGAA
upper sequence: GLYMA04G39500.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G340527_T01 (Zea mays), 3'ss of exon 4
gtatgattacattttaccatacccttttgaaattattatgttttctgtgttttatttttgtaataatgcattagcgaattgatcattgatgatctggggtcttatttaagcgagtgttcatgtgaatttgcagCTGAGTAGTTGCTTCCTTGTGTGTATGAAAGATGATAGTATAGAGGGGATATACGAAACTTTGAAGGAGTGTGCTATCATCAGCAAATCAGCTGGAGGAA
| | ||| || || | | | ||| | | | |||| |||| | | | || | ||| | || ||||| | || || || || ||| | || ||||||||||| || || ||||| || || ||||| |||||||||||||| | || |||||||||||||||||||
-------------------------------------gtactgtct-tgcttcctgccag--acgatgtcattgtgggttgaa-attgtttacttactgtttcttttctgtga---------------tgcagTTAAGCAGCTGTTTTCTTATATGCATGAAAGATGACAGCATTGAGGGAATCTATGAAACCCTGAAGGAGTGTGCTGTAATAAGCAAATCAGCTGGAGGAA
upper sequence: GLYMA04G39500.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0031g01990.t01 (Vitis vinifera), 3'ss of exon 4
-------------------------------gtatgatta---cattttac-catacccttttgaaattatt-atgttttctgtgttttatttttgtaataatgcattagcgaattgatcattgatgatctg----gggtcttatttaagcgagtgttca--tgtgaatttgcagCTGAGTAGTTGCTTCCTTGTGTGTATGAAAGATGATAGTATAGAGGGGATATACGAAACTTTGAAGGAGTGTGCTATCATCAGCAAATCAGCTGGAGGAA
||| | | |||||| | | | ||| || ||||| || || | | || || || |||| |||| | | | | | | || || | | |||||| | || | ||||||||||| ||||||||| | || ||||||||||||||||| || || ||||| || ||| | |||||||||||| | |||||||| || ||||||||||
gtatgtttcacacgcacatgaactagattttatataacttgtccattttcctctttttcttatgtttttatttattacttttattagttgattgtggaatatgctgttaggatcctttgcttgaacagtgtacattggtctttgctaatttctgtgttctgttatgtgctgacagCTGAGTAGCTGCTTCCTTATTTGCATGAAAGATGATAGTATTGAAGGAATATATGACACTCTAAAGGAGTGTGCTGTTATCAGCAAGTCTGCTGGAGGAA
upper sequence: GLYMA04G39500.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S195_46V6.1 (Physcomitrella patens), 3'ss of exon 3
gtatga-ttacattttaccatacccttttgaaattattatgttttctgtgttttatttttgtaataatgcattagcgaattgatcattgatgatctggggtcttatttaagcgagtgttcatgt--gaatttgcagCTGAGTAGTTGCTTCCTTGTGTGTATGAAAGATGATAGTATAGAGGGGATATACGAAACTTTGAAGGAGTGTGCTATCATCAGCAAATCAGCTGGAGGAA
||| || || | || | | | || || || ||| | | ||||||||| || || | | | | ||| | | || ||| | | ||| | | || ||| | | |||||||| |||||||||||||| || | |||| || || || ||||| || ||||| ||| |||||||||||||| | || ||||| |||||||| ||||
gtaggacttgcgttccaattcaactggatgccatggttgcaattttt-tattttatttt-gttttacttcttc--cctcttggtgggcggtgtaatggaaggt-acttatacctggcttggtgttcgggcgtccagCTGAGCAGTTGCTTCCTTGTATGCACCAAAGGCGACAGCATTGAGGGTATCTACGACACTCTGAAGGAGTGTGCTGTTATTAGCAAGTCAGCTGGTGGAA
upper sequence: GLYMA04G39500.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S64_38V6.1 (Physcomitrella patens), 3'ss of exon 3
gtatgattacattttaccatacccttttgaaattattatgttttctgtgttttatttttgtaataatgcattagcgaattgatcattgatgatctggggtcttatttaagcgagtgttcatgtgaatttgcagCTGAGTAGTTGCTTCCTTGTGTGTATGAAAGATGATAGTATAGAGGGGATATACGAAACTTTGAAGGAGTGTGCTATCATCAGCAAATCAGCTGGAGGAA
|| | || | |||| || || | |||| | | | || ||| || ||| | ||| | || || || | ||||| || |||||||| || || || ||||| |||| |||||| |||| ||||| |||||||| ||||| || |||||||||||||| | || ||||| || || || || |
-----------------------gttcggctatctattccttttgtgcgtgcgctctttgcactgaacca--agc---ctggtcagtcgtgaatgcgagtactaatt----ggttgttcgaatg---ttgcagCTAAGCAGCTGTTTCCTACTGTGCATGAAAAATGACAGTATTGAGGGGATTTACGATACCCTGAAGGAGTGTGCTGTAATTAGCAAGTCGGCCGGTGGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgatcattgatgatctggggtcttatttaagcgagtgttcatgtgaatttgcagCTGAGTAGTTGCTTCCTTGTGTGTATGAAAGATGATAGTATAGAGGGGATATACGAAACTTTGAAGGAGTGTGCTATCATCAGCAAATCAGCTGGAGGAA
cattgat putative branch site (score: 4)
tcttatttaa TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgattacattttaccatacccttttgaaattattatgttttctgtgttttatttttgtaataatgcattagcgaattgatcattgatgatctggggtcttatttaagcgagtgttcatgtgaatttgcagCTGAGTAGTTGCTTCCTTGTGTGTATGAAAGATGATAGTATAGAGGGGATATACGAAACTTTGAAGGAGTGTGCTATCATCAGCAAATCAGCTGGAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA